Genomic evidence for the parallel regression of melatonin synthesis and signaling pathways in placental mammals

• Main Authors: Emerling, Christopher A., Springer, Mark S., Gatesy, John, Jones, Zachary, Hamilton, Deana, Xia-Zhu, David, Collin, Matthew A., Delsuc, Frédéric
• Format: Other/Unknown Material
• Language: English
• Published: Zenodo 2021
• Subjects: Mammals; Melatonin pathway; Molecular evolution; Pseudogenes; Convergence; Pineal gland; Crocodilians; bowhead whale
• Online Access: https://doi.org/10.5281/zenodo.4894212

Supplementary Material for: Emerling C.A., Springer M.S., Gatesy J., Jones Z., Hamilton D., Xia-Zhu D., Collin M.A.,and Delsuc F. (2021).Genomic evidence for the parallel regression of melatonin synthesis and signaling pathways in placental mammals. Open Research Europe. Supplementary File Legends: - Supplementary_Figure_S1.pdf: RAxML AANAT gene tree. - Supplementary_Figure_S2.pdf: RAxML ASMT gene tree. - Supplementary_Figure_S3.pdf: RAxML MTNR1A+MTNR1Btree. - Supplementary_Figure_S4.pdf: PAML AANAT results, model 1 (see Supplementary Table S7). - Supplementary_Figure_S5.pdf: PAML ASMT results, model 2 (see Supplementary Table S8). - Supplementary_Figure_S6.pdf: PAML MTNR1A results, model 1 (see Supplementary Table S9). - Supplementary_Figure_S7.pdf: PAML MTNR1B results, model 1 (see Supplementary Table S10). - Supplementary_Table_S1.xlsx: List of species examined in this study and the sources of the genes. Source key: WGS: Sequences derived from NCBI's Whole Genome Shotgun database; Whole Genome Sequencing of Short Reads: whole genomes were sequenced using short-read technologies. The methodologies varied for the species, and will be published with other projects, so please contact the author(s) for information on the specific methodology and samples used; SRA: sequences derived from NCBI's Sequence Read Archive; GenBank: sequences derived from NCBI's nucleotide collection; Bowhead Whale Genome Resource: sequences derived from http://www.bowhead-whale.org; Ensembl: sequences derived from Ensembl genome browser (www.ensembl.org)l; Discovar de novo: sequences derived genomes assembled via Discovar de novo (https://software.broadinstitute.org/software/discovar/blog/). - Supplementary_Table_S2.xlsx: Accession numbers and functionality of AANAT in species examined. Parentheses after accession number indicates coordinates for sequence on the contig / scaffold. Exon colors code for the following: green = putatively functional; yellow = missing; pink = one or more inactivating mutations found. Abbreviations for ...